From e05e5373d038d054acffee1623c59583670afb30 Mon Sep 17 00:00:00 2001 From: borealBytes Date: Thu, 19 Feb 2026 18:29:14 -0500 Subject: [PATCH] fix(attribution): correct source repo URL to SuperiorByteWorks-LLC/agent-project MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit All 40 references to borealBytes/opencode updated to the correct source: https://github.com/SuperiorByteWorks-LLC/agent-project Affected files: SKILL.md, all 24 diagram guides, 9 templates, issue and PR docs, plus assets/examples/example-research-report.md (new file). The example report demonstrates full skill usage: flowchart, sequence, timeline, xychart, radar diagrams — all with accTitle/accDescr and classDef colors, no %%{init}. Covers HEK293T CRISPR editing efficiency as a realistic scientific context. --- .../issue-00000001-markdown-mermaid-skill.md | 4 +- .../pr/pr-00000001-markdown-mermaid-skill.md | 4 +- .../markdown-mermaid-writing/SKILL.md | 6 +- .../examples/example-research-report.md | 218 ++++++++++++++++++ .../references/diagrams/architecture.md | 2 +- .../references/diagrams/block.md | 2 +- .../references/diagrams/c4.md | 2 +- .../references/diagrams/class.md | 2 +- .../references/diagrams/complex_examples.md | 2 +- .../references/diagrams/er.md | 2 +- .../references/diagrams/flowchart.md | 2 +- .../references/diagrams/gantt.md | 2 +- .../references/diagrams/git_graph.md | 2 +- .../references/diagrams/kanban.md | 2 +- .../references/diagrams/mindmap.md | 2 +- .../references/diagrams/packet.md | 2 +- .../references/diagrams/pie.md | 2 +- .../references/diagrams/quadrant.md | 2 +- .../references/diagrams/radar.md | 2 +- .../references/diagrams/requirement.md | 2 +- .../references/diagrams/sankey.md | 2 +- .../references/diagrams/sequence.md | 2 +- .../references/diagrams/state.md | 2 +- .../references/diagrams/timeline.md | 2 +- .../references/diagrams/treemap.md | 2 +- .../references/diagrams/user_journey.md | 2 +- .../references/diagrams/xy_chart.md | 2 +- .../references/diagrams/zenuml.md | 2 +- .../references/markdown_style_guide.md | 2 +- .../references/mermaid_style_guide.md | 2 +- .../templates/decision_record.md | 2 +- .../templates/how_to_guide.md | 4 +- .../templates/issue.md | 2 +- .../templates/kanban.md | 2 +- .../templates/presentation.md | 2 +- .../templates/project_documentation.md | 2 +- .../templates/pull_request.md | 2 +- .../templates/research_paper.md | 2 +- .../templates/status_report.md | 2 +- 39 files changed, 261 insertions(+), 43 deletions(-) create mode 100644 scientific-skills/markdown-mermaid-writing/assets/examples/example-research-report.md diff --git a/docs/project/issues/issue-00000001-markdown-mermaid-skill.md b/docs/project/issues/issue-00000001-markdown-mermaid-skill.md index 71d4999..e2192e2 100644 --- a/docs/project/issues/issue-00000001-markdown-mermaid-skill.md +++ b/docs/project/issues/issue-00000001-markdown-mermaid-skill.md @@ -116,7 +116,7 @@ flowchart LR ### Content sources -All style guides and templates ported from the `borealBytes/opencode` repository under Apache-2.0 license with attribution retained[^3]. +All style guides and templates ported from the `SuperiorByteWorks-LLC/agent-project` repository under Apache-2.0 license with attribution retained[^3]. | Source path | Destination | | ------------------------------------------- | ---------------------------------------------------- | @@ -154,7 +154,7 @@ scientific-skills/markdown-mermaid-writing/ [^2]: Orion Li (K-Dense), responding: "Thanks for letting us know! We'll make sure to include this into our sauce when we implement our upcoming reorganization of the skills." — K-Dense Discord, 2026-02-19. -[^3]: Boreal Bytes / Superior Byte Works, LLC. `opencode` repository. https://github.com/borealBytes/opencode. Apache-2.0 License. +[^3]: Boreal Bytes / Superior Byte Works, LLC. `opencode` repository. https://github.com/SuperiorByteWorks-LLC/agent-project. Apache-2.0 License. --- diff --git a/docs/project/pr/pr-00000001-markdown-mermaid-skill.md b/docs/project/pr/pr-00000001-markdown-mermaid-skill.md index bc75578..1f49b15 100644 --- a/docs/project/pr/pr-00000001-markdown-mermaid-skill.md +++ b/docs/project/pr/pr-00000001-markdown-mermaid-skill.md @@ -16,7 +16,7 @@ ### What changed and why -This PR adds a new skill — `markdown-mermaid-writing` — that establishes markdown with embedded Mermaid diagrams as the **default and canonical documentation format** for all scientific skills. The skill ports comprehensive style guides, 24 diagram type references, and 9 document templates from the `borealBytes/opencode` project, and codifies the "source format" philosophy proposed in the K-Dense Discord on 2026-02-19. +This PR adds a new skill — `markdown-mermaid-writing` — that establishes markdown with embedded Mermaid diagrams as the **default and canonical documentation format** for all scientific skills. The skill ports comprehensive style guides, 24 diagram type references, and 9 document templates from the `SuperiorByteWorks-LLC/agent-project` project, and codifies the "source format" philosophy proposed in the K-Dense Discord on 2026-02-19. The motivation: scientific outputs currently default to Python-generated or AI-generated images for diagrams. This PR inverts that priority — text-based Mermaid diagrams are the source of truth, downstream image generation is secondary. This gives users version-controlled, token-efficient, universally renderable documentation by default. @@ -179,7 +179,7 @@ No ADR created — this is a documentation addition with no architectural tradeo ## 🔗 References - [Issue #00000001](../issues/issue-00000001-markdown-mermaid-skill.md) — Feature request -- [opencode repository](https://github.com/borealBytes/opencode) — Source of ported style guides (Apache-2.0) +- [opencode repository](https://github.com/SuperiorByteWorks-LLC/agent-project) — Source of ported style guides (Apache-2.0) - [K-Dense Discord thread](https://discord.com/channels/k-dense) — Originating conversation, 2026-02-19 --- diff --git a/scientific-skills/markdown-mermaid-writing/SKILL.md b/scientific-skills/markdown-mermaid-writing/SKILL.md index 8c10893..1d17db5 100644 --- a/scientific-skills/markdown-mermaid-writing/SKILL.md +++ b/scientific-skills/markdown-mermaid-writing/SKILL.md @@ -12,7 +12,7 @@ allowed-tools: [Read, Write, Edit, Bash] license: Apache-2.0 metadata: skill-author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) - skill-source: https://github.com/borealBytes/opencode + skill-source: https://github.com/SuperiorByteWorks-LLC/agent-project skill-version: "1.0.0" skill-contributors: - name: Clayton Young @@ -273,9 +273,9 @@ Each file contains: production-quality exemplar, tips specific to that type, and ## 📝 Attribution -All style guides, diagram type guides, and document templates in this skill are ported from the `borealBytes/opencode` repository under the Apache-2.0 License. +All style guides, diagram type guides, and document templates in this skill are ported from the `SuperiorByteWorks-LLC/agent-project` repository under the Apache-2.0 License. -- **Source**: https://github.com/borealBytes/opencode +- **Source**: https://github.com/SuperiorByteWorks-LLC/agent-project - **Author**: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) - **License**: Apache-2.0 diff --git a/scientific-skills/markdown-mermaid-writing/assets/examples/example-research-report.md b/scientific-skills/markdown-mermaid-writing/assets/examples/example-research-report.md new file mode 100644 index 0000000..e470e73 --- /dev/null +++ b/scientific-skills/markdown-mermaid-writing/assets/examples/example-research-report.md @@ -0,0 +1,218 @@ +# CRISPR-Based Gene Editing Efficiency Analysis + +_Example research report — demonstrates markdown-mermaid-writing skill standards. All diagrams use Mermaid embedded in markdown as the source format._ + +--- + +## 📋 Overview + +This report analyzes the efficiency of CRISPR-Cas9 gene editing across three cell line models under variable guide RNA (gRNA) conditions. Editing efficiency was quantified by T7E1 assay and next-generation sequencing (NGS) of on-target loci[^1]. + +**Key findings:** + +- HEK293T cells show highest editing efficiency (mean 78%) across all gRNA designs +- GC content between 40–65% correlates with editing efficiency (r = 0.82) +- Off-target events occur at <0.1% frequency across all conditions tested + +--- + +## 🔄 Experimental workflow + +CRISPR editing experiments followed a standardized five-stage protocol. Each stage has defined go/no-go criteria before proceeding. + +```mermaid +flowchart TD + accTitle: CRISPR Editing Experimental Workflow + accDescr: Five-stage experimental pipeline from gRNA design through data analysis, with quality checkpoints between each stage. + + design["🧬 Stage 1\ngRNA Design\n(CRISPRscan + Cas-OFFinder)"] + synth["⚙️ Stage 2\nOligo Synthesis\n& Annealing"] + transfect["🔬 Stage 3\nCell Transfection\n(Lipofectamine 3000)"] + screen["🧪 Stage 4\nPrimary Screen\n(T7E1 assay)"] + ngs["📊 Stage 5\nNGS Validation\n(150 bp PE reads)"] + + qc1{GC 40-65%?} + qc2{Yield ≥ 2 µg?} + qc3{Viability ≥ 85%?} + qc4{Band visible?} + + design --> qc1 + qc1 -->|"✅ Pass"| synth + qc1 -->|"❌ Redesign"| design + synth --> qc2 + qc2 -->|"✅ Pass"| transfect + qc2 -->|"❌ Re-synthesize"| synth + transfect --> qc3 + qc3 -->|"✅ Pass"| screen + qc3 -->|"❌ Optimize"| transfect + screen --> qc4 + qc4 -->|"✅ Pass"| ngs + qc4 -->|"❌ Repeat"| screen + + classDef stage fill:#dbeafe,stroke:#2563eb,stroke-width:2px,color:#1e3a5f + classDef gate fill:#fef9c3,stroke:#ca8a04,stroke-width:2px,color:#713f12 + classDef fail fill:#fee2e2,stroke:#dc2626,stroke-width:2px,color:#7f1d1d + + class design,synth,transfect,screen,ngs stage + class qc1,qc2,qc3,qc4 gate +``` + +--- + +## 🔬 Methods + +### Cell lines and culture + +Three cell lines were used: HEK293T (human embryonic kidney), K562 (chronic myelogenous leukemia), and Jurkat (T-lymphocyte). All lines were maintained in RPMI-1640 with 10% FBS at 37°C / 5% CO₂[^2]. + +### gRNA design and efficiency prediction + +gRNAs targeting the _EMX1_ locus were designed using CRISPRscan[^3] with the following criteria: + +| Criterion | Threshold | Rationale | +| -------------------- | --------- | ------------------------------------- | +| GC content | 40–65% | Optimal Tm and Cas9 binding | +| CRISPRscan score | ≥ 0.6 | Predicted on-target activity | +| Off-target sites | ≤ 5 (≤3 mismatches) | Reduce off-target editing risk | +| Homopolymer runs | None (>4 nt) | Prevents premature transcription stop | + +### Transfection protocol + +RNP complexes were assembled at 1:1.2 molar ratio (Cas9:gRNA) and delivered by lipofection. Cells were harvested 72 hours post-transfection for genomic DNA extraction. + +### Analysis pipeline + +```mermaid +sequenceDiagram + accTitle: NGS Data Analysis Pipeline + accDescr: Sequence of computational steps from raw FASTQ files through variant calling to final efficiency report. + + participant raw as 📥 Raw FASTQ + participant qc as 🔍 FastQC + participant trim as ✂️ Trimmomatic + participant align as 🗺️ BWA-MEM2 + participant call as ⚙️ CRISPResso2 + participant report as 📊 Report + + raw->>qc: Per-base quality scores + qc-->>trim: Flag low-Q reads (Q<20) + trim->>align: Cleaned reads + align->>align: Index reference genome (hg38) + align->>call: BAM + target region BED + call->>call: Quantify indel frequency + call-->>report: Editing efficiency (%) + call-->>report: Off-target events + report-->>report: Statistical summary +``` + +--- + +## 📊 Results + +### Editing efficiency by cell line + +| Cell line | n (replicates) | Mean efficiency (%) | SD (%) | Range (%) | +| ---------- | -------------- | ------------------- | ------ | --------- | +| **HEK293T** | 6 | **78.4** | 4.2 | 71.2–84.6 | +| K562 | 6 | 52.1 | 8.7 | 38.4–63.2 | +| Jurkat | 6 | 31.8 | 11.3 | 14.2–47.5 | + +HEK293T cells showed significantly higher editing efficiency than both K562 (p < 0.001) and Jurkat (p < 0.001) lines by one-way ANOVA with Tukey post-hoc correction. + +### Effect of GC content on efficiency + +GC content between 40–65% was strongly correlated with editing efficiency (Pearson r = 0.82, p < 0.0001, n = 48 gRNAs). + +```mermaid +xychart-beta + accTitle: Editing Efficiency vs gRNA GC Content + accDescr: Bar chart showing mean editing efficiency grouped by GC content bins, demonstrating optimal performance in the 40 to 65 percent GC range + + title "Mean Editing Efficiency by GC Content Bin (HEK293T)" + x-axis ["< 30%", "30–40%", "40–50%", "50–65%", "> 65%"] + y-axis "Editing Efficiency (%)" 0 --> 100 + bar [18, 42, 76, 81, 38] +``` + +### Timeline of key experimental milestones + +```mermaid +timeline + accTitle: Experiment Timeline — CRISPR Efficiency Study + accDescr: Chronological milestones from study design through manuscript submission across six months + + section Month 1 + Study design and gRNA library design : 48 gRNAs across 3 target loci + Cell line authentication : STR profiling confirmed all three lines + section Month 2 + gRNA synthesis and QC : 46/48 gRNAs passed yield threshold + Pilot transfections (HEK293T) : Optimized lipofection conditions + section Month 3 + Full transfection series : All 3 cell lines, all 46 gRNAs, 6 replicates + T7E1 primary screening : Passed go/no-go for all conditions + section Month 4 + NGS library preparation : 276 samples processed + Sequencing run (NovaSeq) : 150 bp PE, mean 50k reads/sample + section Month 5 + Bioinformatic analysis : CRISPResso2 pipeline + Statistical analysis : ANOVA, correlation, regression + section Month 6 + Manuscript preparation : This report +``` + +--- + +## 🔍 Discussion + +### Why HEK293T outperforms suspension lines + +HEK293T's superior editing efficiency relative to K562 and Jurkat likely reflects three factors[^4]: + +1. **Adherent morphology** — enables more uniform lipofection contact +2. **High transfection permissiveness** — HEK293T expresses the SV40 large T antigen, which may facilitate nuclear import +3. **Cell cycle distribution** — higher proportion in S/G2 phase where HDR is favored + +
+🔧 Technical details — off-target analysis + +Off-target editing was assessed by GUIDE-seq at the 5 highest-activity gRNAs. No off-target sites exceeding 0.1% editing frequency were detected. The three potential sites flagged by Cas-OFFinder (≤2 mismatches) showed 0.00%, 0.02%, and 0.04% indel frequencies — all below the assay noise floor of 0.05%. + +Full GUIDE-seq data available in supplementary data package (GEO accession pending). + +
+ +--- + +### Comparison with published benchmarks + +```mermaid +radar + accTitle: CRISPR Method Comparison Radar + accDescr: Multi-dimensional radar chart comparing our protocol against published Cas9 and base editing benchmarks across five performance axes + + title Performance vs. Published Methods + x-axis ["Efficiency", "Specificity", "Delivery ease", "Cost", "Cell viability"] + "This study (RNP + Lipo)" : [78, 95, 80, 85, 90] + "Plasmid Cas9 (lit.)" : [55, 70, 90, 95, 75] + "Electroporation RNP (lit.)" : [88, 96, 50, 60, 65] +``` + +--- + +## 🎯 Conclusions + +1. RNP-lipofection in HEK293T achieves >75% CRISPR editing efficiency — competitive with electroporation without the associated viability cost +2. gRNA GC content is the single strongest predictor of editing efficiency in our dataset (r = 0.82) +3. This protocol is not directly transferable to suspension lines without further optimization; K562 and Jurkat require electroporation or viral delivery for comparable efficiency + +--- + +## 🔗 References + +[^1]: Ran, F.A. et al. (2013). "Genome engineering using the CRISPR-Cas9 system." _Nature Protocols_, 8(11), 2281–2308. https://doi.org/10.1038/nprot.2013.143 + +[^2]: ATCC. (2024). "Cell Line Authentication and Quality Control." https://www.atcc.org/resources/technical-documents/cell-line-authentication + +[^3]: Moreno-Mateos, M.A. et al. (2015). "CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo." _Nature Methods_, 12(10), 982–988. https://doi.org/10.1038/nmeth.3543 + +[^4]: Molla, K.A. & Yang, Y. (2019). "CRISPR/Cas-Mediated Base Editing: Technical Considerations and Practical Applications." _Trends in Biotechnology_, 37(10), 1121–1142. https://doi.org/10.1016/j.tibtech.2019.03.008 diff --git a/scientific-skills/markdown-mermaid-writing/references/diagrams/architecture.md b/scientific-skills/markdown-mermaid-writing/references/diagrams/architecture.md index 2067bc6..8f32130 100644 --- a/scientific-skills/markdown-mermaid-writing/references/diagrams/architecture.md +++ b/scientific-skills/markdown-mermaid-writing/references/diagrams/architecture.md @@ -1,4 +1,4 @@ - + # Architecture Diagram diff --git a/scientific-skills/markdown-mermaid-writing/references/diagrams/block.md b/scientific-skills/markdown-mermaid-writing/references/diagrams/block.md index 6310b3c..7009eb9 100644 --- a/scientific-skills/markdown-mermaid-writing/references/diagrams/block.md +++ b/scientific-skills/markdown-mermaid-writing/references/diagrams/block.md @@ -1,4 +1,4 @@ - + # Block Diagram diff --git a/scientific-skills/markdown-mermaid-writing/references/diagrams/c4.md b/scientific-skills/markdown-mermaid-writing/references/diagrams/c4.md index c046f29..6ae5117 100644 --- a/scientific-skills/markdown-mermaid-writing/references/diagrams/c4.md +++ b/scientific-skills/markdown-mermaid-writing/references/diagrams/c4.md @@ -1,4 +1,4 @@ - + # C4 Diagram diff --git a/scientific-skills/markdown-mermaid-writing/references/diagrams/class.md b/scientific-skills/markdown-mermaid-writing/references/diagrams/class.md index dcab409..a93eb08 100644 --- a/scientific-skills/markdown-mermaid-writing/references/diagrams/class.md +++ b/scientific-skills/markdown-mermaid-writing/references/diagrams/class.md @@ -1,4 +1,4 @@ - + # Class Diagram diff --git a/scientific-skills/markdown-mermaid-writing/references/diagrams/complex_examples.md b/scientific-skills/markdown-mermaid-writing/references/diagrams/complex_examples.md index 6a37fa6..919c32d 100644 --- a/scientific-skills/markdown-mermaid-writing/references/diagrams/complex_examples.md +++ b/scientific-skills/markdown-mermaid-writing/references/diagrams/complex_examples.md @@ -1,4 +1,4 @@ - + # Composing Complex Diagram Sets diff --git a/scientific-skills/markdown-mermaid-writing/references/diagrams/er.md b/scientific-skills/markdown-mermaid-writing/references/diagrams/er.md index 167080d..140352d 100644 --- a/scientific-skills/markdown-mermaid-writing/references/diagrams/er.md +++ b/scientific-skills/markdown-mermaid-writing/references/diagrams/er.md @@ -1,4 +1,4 @@ - + # Entity Relationship (ER) Diagram diff --git a/scientific-skills/markdown-mermaid-writing/references/diagrams/flowchart.md b/scientific-skills/markdown-mermaid-writing/references/diagrams/flowchart.md index 21a036b..9095e37 100644 --- a/scientific-skills/markdown-mermaid-writing/references/diagrams/flowchart.md +++ b/scientific-skills/markdown-mermaid-writing/references/diagrams/flowchart.md @@ -1,4 +1,4 @@ - + # Flowchart diff --git a/scientific-skills/markdown-mermaid-writing/references/diagrams/gantt.md b/scientific-skills/markdown-mermaid-writing/references/diagrams/gantt.md index b564060..217d109 100644 --- a/scientific-skills/markdown-mermaid-writing/references/diagrams/gantt.md +++ b/scientific-skills/markdown-mermaid-writing/references/diagrams/gantt.md @@ -1,4 +1,4 @@ - + # Gantt Chart diff --git a/scientific-skills/markdown-mermaid-writing/references/diagrams/git_graph.md b/scientific-skills/markdown-mermaid-writing/references/diagrams/git_graph.md index 8909407..f851420 100644 --- a/scientific-skills/markdown-mermaid-writing/references/diagrams/git_graph.md +++ b/scientific-skills/markdown-mermaid-writing/references/diagrams/git_graph.md @@ -1,4 +1,4 @@ - + # Git Graph diff --git a/scientific-skills/markdown-mermaid-writing/references/diagrams/kanban.md b/scientific-skills/markdown-mermaid-writing/references/diagrams/kanban.md index 1c39e6a..c3d4b5d 100644 --- a/scientific-skills/markdown-mermaid-writing/references/diagrams/kanban.md +++ b/scientific-skills/markdown-mermaid-writing/references/diagrams/kanban.md @@ -1,4 +1,4 @@ - + # Kanban Board diff --git a/scientific-skills/markdown-mermaid-writing/references/diagrams/mindmap.md b/scientific-skills/markdown-mermaid-writing/references/diagrams/mindmap.md index 6a3317d..61a7b36 100644 --- a/scientific-skills/markdown-mermaid-writing/references/diagrams/mindmap.md +++ b/scientific-skills/markdown-mermaid-writing/references/diagrams/mindmap.md @@ -1,4 +1,4 @@ - + # Mindmap diff --git a/scientific-skills/markdown-mermaid-writing/references/diagrams/packet.md b/scientific-skills/markdown-mermaid-writing/references/diagrams/packet.md index 90ee21c..f858963 100644 --- a/scientific-skills/markdown-mermaid-writing/references/diagrams/packet.md +++ b/scientific-skills/markdown-mermaid-writing/references/diagrams/packet.md @@ -1,4 +1,4 @@ - + # Packet Diagram diff --git a/scientific-skills/markdown-mermaid-writing/references/diagrams/pie.md b/scientific-skills/markdown-mermaid-writing/references/diagrams/pie.md index d75da91..8d3e335 100644 --- a/scientific-skills/markdown-mermaid-writing/references/diagrams/pie.md +++ b/scientific-skills/markdown-mermaid-writing/references/diagrams/pie.md @@ -1,4 +1,4 @@ - + # Pie Chart diff --git a/scientific-skills/markdown-mermaid-writing/references/diagrams/quadrant.md b/scientific-skills/markdown-mermaid-writing/references/diagrams/quadrant.md index 9ba0a56..660e8f2 100644 --- a/scientific-skills/markdown-mermaid-writing/references/diagrams/quadrant.md +++ b/scientific-skills/markdown-mermaid-writing/references/diagrams/quadrant.md @@ -1,4 +1,4 @@ - + # Quadrant Chart diff --git a/scientific-skills/markdown-mermaid-writing/references/diagrams/radar.md b/scientific-skills/markdown-mermaid-writing/references/diagrams/radar.md index f69787f..e8ee8cd 100644 --- a/scientific-skills/markdown-mermaid-writing/references/diagrams/radar.md +++ b/scientific-skills/markdown-mermaid-writing/references/diagrams/radar.md @@ -1,4 +1,4 @@ - + # Radar Chart diff --git a/scientific-skills/markdown-mermaid-writing/references/diagrams/requirement.md b/scientific-skills/markdown-mermaid-writing/references/diagrams/requirement.md index 9e7db70..d88ff70 100644 --- a/scientific-skills/markdown-mermaid-writing/references/diagrams/requirement.md +++ b/scientific-skills/markdown-mermaid-writing/references/diagrams/requirement.md @@ -1,4 +1,4 @@ - + # Requirement Diagram diff --git a/scientific-skills/markdown-mermaid-writing/references/diagrams/sankey.md b/scientific-skills/markdown-mermaid-writing/references/diagrams/sankey.md index 4dc9d31..acfebfc 100644 --- a/scientific-skills/markdown-mermaid-writing/references/diagrams/sankey.md +++ b/scientific-skills/markdown-mermaid-writing/references/diagrams/sankey.md @@ -1,4 +1,4 @@ - + # Sankey Diagram diff --git a/scientific-skills/markdown-mermaid-writing/references/diagrams/sequence.md b/scientific-skills/markdown-mermaid-writing/references/diagrams/sequence.md index a83a010..71bf43c 100644 --- a/scientific-skills/markdown-mermaid-writing/references/diagrams/sequence.md +++ b/scientific-skills/markdown-mermaid-writing/references/diagrams/sequence.md @@ -1,4 +1,4 @@ - + # Sequence Diagram diff --git a/scientific-skills/markdown-mermaid-writing/references/diagrams/state.md b/scientific-skills/markdown-mermaid-writing/references/diagrams/state.md index 891a347..d142b5a 100644 --- a/scientific-skills/markdown-mermaid-writing/references/diagrams/state.md +++ b/scientific-skills/markdown-mermaid-writing/references/diagrams/state.md @@ -1,4 +1,4 @@ - + # State Diagram diff --git a/scientific-skills/markdown-mermaid-writing/references/diagrams/timeline.md b/scientific-skills/markdown-mermaid-writing/references/diagrams/timeline.md index 58f0353..2465689 100644 --- a/scientific-skills/markdown-mermaid-writing/references/diagrams/timeline.md +++ b/scientific-skills/markdown-mermaid-writing/references/diagrams/timeline.md @@ -1,4 +1,4 @@ - + # Timeline diff --git a/scientific-skills/markdown-mermaid-writing/references/diagrams/treemap.md b/scientific-skills/markdown-mermaid-writing/references/diagrams/treemap.md index 779e64e..c081804 100644 --- a/scientific-skills/markdown-mermaid-writing/references/diagrams/treemap.md +++ b/scientific-skills/markdown-mermaid-writing/references/diagrams/treemap.md @@ -1,4 +1,4 @@ - + # Treemap Diagram diff --git a/scientific-skills/markdown-mermaid-writing/references/diagrams/user_journey.md b/scientific-skills/markdown-mermaid-writing/references/diagrams/user_journey.md index aa09966..c9faadc 100644 --- a/scientific-skills/markdown-mermaid-writing/references/diagrams/user_journey.md +++ b/scientific-skills/markdown-mermaid-writing/references/diagrams/user_journey.md @@ -1,4 +1,4 @@ - + # User Journey diff --git a/scientific-skills/markdown-mermaid-writing/references/diagrams/xy_chart.md b/scientific-skills/markdown-mermaid-writing/references/diagrams/xy_chart.md index f93ff7a..82c159b 100644 --- a/scientific-skills/markdown-mermaid-writing/references/diagrams/xy_chart.md +++ b/scientific-skills/markdown-mermaid-writing/references/diagrams/xy_chart.md @@ -1,4 +1,4 @@ - + # XY Chart diff --git a/scientific-skills/markdown-mermaid-writing/references/diagrams/zenuml.md b/scientific-skills/markdown-mermaid-writing/references/diagrams/zenuml.md index be59979..fba0161 100644 --- a/scientific-skills/markdown-mermaid-writing/references/diagrams/zenuml.md +++ b/scientific-skills/markdown-mermaid-writing/references/diagrams/zenuml.md @@ -1,4 +1,4 @@ - + # ZenUML Sequence Diagram diff --git a/scientific-skills/markdown-mermaid-writing/references/markdown_style_guide.md b/scientific-skills/markdown-mermaid-writing/references/markdown_style_guide.md index 2f23272..952b733 100644 --- a/scientific-skills/markdown-mermaid-writing/references/markdown_style_guide.md +++ b/scientific-skills/markdown-mermaid-writing/references/markdown_style_guide.md @@ -1,4 +1,4 @@ - + # Markdown Style Guide diff --git a/scientific-skills/markdown-mermaid-writing/references/mermaid_style_guide.md b/scientific-skills/markdown-mermaid-writing/references/mermaid_style_guide.md index 2427462..16246e9 100644 --- a/scientific-skills/markdown-mermaid-writing/references/mermaid_style_guide.md +++ b/scientific-skills/markdown-mermaid-writing/references/mermaid_style_guide.md @@ -1,4 +1,4 @@ - + # Mermaid Diagram Style Guide diff --git a/scientific-skills/markdown-mermaid-writing/templates/decision_record.md b/scientific-skills/markdown-mermaid-writing/templates/decision_record.md index 4eb6a57..8b831d6 100644 --- a/scientific-skills/markdown-mermaid-writing/templates/decision_record.md +++ b/scientific-skills/markdown-mermaid-writing/templates/decision_record.md @@ -1,4 +1,4 @@ - + # Decision Record (ADR/RFC) Template diff --git a/scientific-skills/markdown-mermaid-writing/templates/how_to_guide.md b/scientific-skills/markdown-mermaid-writing/templates/how_to_guide.md index 2a75e8a..62f4fd8 100644 --- a/scientific-skills/markdown-mermaid-writing/templates/how_to_guide.md +++ b/scientific-skills/markdown-mermaid-writing/templates/how_to_guide.md @@ -1,4 +1,4 @@ - + # How-To / Tutorial Guide Template @@ -268,7 +268,7 @@ Key commands and values from this guide for future reference: ## 🔗 References - [Official documentation](https://example.com) — [Which section is most relevant] -- [Source repository](https://github.com/borealBytes) — [For bug reports and contributions] +- [Source repository](https://github.com/SuperiorByteWorks-LLC) — [For bug reports and contributions] --- diff --git a/scientific-skills/markdown-mermaid-writing/templates/issue.md b/scientific-skills/markdown-mermaid-writing/templates/issue.md index 421332c..79b77a6 100644 --- a/scientific-skills/markdown-mermaid-writing/templates/issue.md +++ b/scientific-skills/markdown-mermaid-writing/templates/issue.md @@ -1,4 +1,4 @@ - + # Issue Documentation Template diff --git a/scientific-skills/markdown-mermaid-writing/templates/kanban.md b/scientific-skills/markdown-mermaid-writing/templates/kanban.md index da36e37..e95aeeb 100644 --- a/scientific-skills/markdown-mermaid-writing/templates/kanban.md +++ b/scientific-skills/markdown-mermaid-writing/templates/kanban.md @@ -1,4 +1,4 @@ - + # Kanban Board Documentation Template diff --git a/scientific-skills/markdown-mermaid-writing/templates/presentation.md b/scientific-skills/markdown-mermaid-writing/templates/presentation.md index 9bb2de6..757186a 100644 --- a/scientific-skills/markdown-mermaid-writing/templates/presentation.md +++ b/scientific-skills/markdown-mermaid-writing/templates/presentation.md @@ -1,4 +1,4 @@ - + # Presentation / Briefing Template diff --git a/scientific-skills/markdown-mermaid-writing/templates/project_documentation.md b/scientific-skills/markdown-mermaid-writing/templates/project_documentation.md index aa37bb1..8c903cf 100644 --- a/scientific-skills/markdown-mermaid-writing/templates/project_documentation.md +++ b/scientific-skills/markdown-mermaid-writing/templates/project_documentation.md @@ -1,4 +1,4 @@ - + # Project Documentation Template diff --git a/scientific-skills/markdown-mermaid-writing/templates/pull_request.md b/scientific-skills/markdown-mermaid-writing/templates/pull_request.md index 5e21f39..d22b0a1 100644 --- a/scientific-skills/markdown-mermaid-writing/templates/pull_request.md +++ b/scientific-skills/markdown-mermaid-writing/templates/pull_request.md @@ -1,4 +1,4 @@ - + # Pull Request Documentation Template diff --git a/scientific-skills/markdown-mermaid-writing/templates/research_paper.md b/scientific-skills/markdown-mermaid-writing/templates/research_paper.md index 2e4e27b..3ccb3eb 100644 --- a/scientific-skills/markdown-mermaid-writing/templates/research_paper.md +++ b/scientific-skills/markdown-mermaid-writing/templates/research_paper.md @@ -1,4 +1,4 @@ - + # Research Paper / Technical Analysis Template diff --git a/scientific-skills/markdown-mermaid-writing/templates/status_report.md b/scientific-skills/markdown-mermaid-writing/templates/status_report.md index d653225..6b11eb1 100644 --- a/scientific-skills/markdown-mermaid-writing/templates/status_report.md +++ b/scientific-skills/markdown-mermaid-writing/templates/status_report.md @@ -1,4 +1,4 @@ - + # Status Report / Executive Briefing Template